Inflammatory bowel disease (IBD) is an inflammatory condition of the digestive tract not caused by infectious agents. Symptoms of IBD, such as diarrhea and pain, diminish one's quality of life. Underlying immune dysregulation may put IBD patients at risk for severe infectious disease making preventative vaccination highly recommended. Therefore, this study sought to assess rates of pneumococcal vaccination in patients with IBD.A cross-sectional observational study was employed utilizing administrative data extracts from the Veterans Health Administration (VHA) to identify patients diagnosed with IBD per International Classification of Diseases, Version 9, Clinical Modification codes. Their pneumococcal vaccine histories were determined from Common Procedural Terminology codes. Data were aggregated to the patient level and subjected to multivariable logistic regression to assess factors associated with receipt of the vaccination and 1-year mortality; survival analyses extended follow-up to as much as 4 years following IBD diagnosis.From October 2004 to September 2009, 49,350 patients were diagnosed with IBD in the VHA. Incidence was approximately 6000 cases/y. Patients averaged 62 years (±15, range 19–98) with 45% aged 65 or older. Approximately 6% were women, 21% were highly disabled from a military service-connected condition, 46% had hypertension, 38% dyslipidemia, and 18% diabetes. Only 20% of the cohort received pneumococcal vaccination including 5% vaccinated prior to IBD diagnosis, 2% on the date of diagnosis, and 13% subsequently. Being married, living outside the Northeast, and having more comorbidities were associated with vaccination before IBD diagnosis; models of vaccination at or after diagnosis demonstrated poor fit: little better than chance. Vaccinations before, after, and at diagnosis were protective against 1-year mortality adjusting for clinical and demographic covariates. Living in the South was an independent risk factor for death among IBD patients.While vaccination for pneumococcus is a low-cost, low-risk recommendation for persons with IBD with an apparent survival benefit, vaccination rates were low.